The Aquatic Warbler Acrocephalus paludicola is a globally threatened, long-distance migratory passerine that continues to decline in abundance and range. Studies throughout its annual cycle are needed, including during migration, when information on habitat availability and usage are important for conservation. Here, the autumn occurrence (distribution, abundance, phenology) of Aquatic Warblers in Portugal is described taking advantage of an increase in capture effort with diurnal song playback. The species was captured at six new sites and seen at a further three, increasing the total number of sites to 16. Salreu marshlands appeared to be the most important with 93% of all captures since 2009, although ringing effort was highly variable between sites. We show that song playback did not influence age nor sex ratios, but tended to attract individuals with lower body mass, presumably those that arrived recently at stopover sites. Adult males migrated earlier than all other sex and age categories, in accordance with their limited role in parental care. Furthermore, we show that at least some individuals fuel up at Portuguese stopovers, which increases their importance for conservation. In addition, at Salreu marshlands, the abundance of Aquatic Warblers was significantly greater at an active than at a dry, abandoned (extensive) rice field, suggesting this land-use change may affect the quality of stopover sites. Recommendations regarding habitat management and conservation measures are proposed.